Week 6: Eleana

This week marked the end of our co-culture experiment. Monday, after fixing the cells over the weekend we performed flow cytometry. We were able to collect the conditions of our experiment and have multiple replicates. Tuesday we began analyzing this data with Flow Jo. Which requires having compensation controls to help account for any flurochrome spillover which can occur in color channels. We then began setting up for the repeat of this experiment by making more alginate and designing the next experimental setup which will be a repeat of this experiment, and the beginning of our experiment with a breast cancer line and a cell tracking experiment. Wednesday, we placed some breast cancer cells into culture and started making hydrogels. Thursday, we headed back to pathology and covered one case of a patient who had a return of breast cancer after many years that changed type. After pathology, I presented our preliminary data at the Vanpouille-Box meeting, and got insight on how to deal with our data to discover more trends. So far from the analysis, our hydrogels help to proliferate and make our T-cells less exhausted compared to a normal plate coating (antibodies on plate that activate T-cells). We then functionalized are gels with antibodies. Friday, we began T-cell extraction from our cells and seeded them onto their plates. I am continuing to analyze the data and look forward to sharing the results on Tuesday!

Week 6: Aidan

This week I was able to get Amelia and Arina into some of Dr. Kaplitt’s surgery cases on Wednesday, which included a GPI DBS stage one and stage two, and an intrathecal pain pump implantation. 3D print of the flat halbach array was successful, and the print seems very high quality for a first iteration. Unfortunately the epoxy did not arrive in time for me to build the array this week, so I will next week. The goal with this platform is to perform a place-preference tests with mice that have the viral gene expression of ferritin-TRPV1 channel. Prior testing with a simple array of magnets laid on the floor of the chamber demonstrated either no preference or aversion to the magnets. Since the mice have no mechanism we know of to avoid the magnetic field, we hypothesize that the aversion was due to the exposed metal surface of the magnets feeling cold compared to the acrylic behavior chamber. In future testing, we will apply a thin sheet of plastic to the entire chamber to provide a consistent surface feel. 

Week 6: Nina

This week, I went to Dr. Samstein's clinic in Chinatown. These past few weeks, I have only been the clinic and rounds at the main branch of New York Presbyterian Hospital. I learned about the value of community-based care seeing how quite a few patients prefer to stay closer to their place of residence where they are not bound by translation or language barriers. Many patients at the Chinatown location speak English as a second language, therefore, a real-time translation service is provided to patients over the phone. I have shadowed in different hospitals where their translation services occur over a tablet, which allows the patient to see the face and motions of the translator. The services provided at NYP Chinatown for translation are based over call, but it does help that many patients bring family members who can aid in the interpretation of medical information. I learned that there are tablets with translation services at the main hospital, but these are not available at off-site locations. In terms of my summer research project, we are still figuring out logistic details of obtaining or using patient-derived samples from perfused livers in accordance with existing IRB protocols. As my advisor is based at WCM, I will continue this summer immersion project over the course of my PhD.

Week 6: Wendy Zimmerman

 This week I independently performed RNA isolations on Monday, Thursday, and Friday, which has gotten me through the tendon samples of an experiment in laxity with PTOA. I will complete my assigned samples for isolation next week. On Tuesday, I was able to shadow Dr. Rodeo in the OR where I saw a rotator cuff repair with the addition of bone marrow aspirate from the patient's iliac crest injected combined with clotting factors. It was interesting to see this technique used and discuss with Dr. Rodeo the components of the treatment and science behind it. I also saw an arthrotomy with arthroscopic remplissage and an open hagl repair, and irrigation and debridement after a patellar tendon repair. On Wednesday, I shadowed Dr. Eliasberg in the clinic and got to ask her and her PA questions about the various approaches and reasonings behind medical decisions. I am looking forward to next week, where I will shadow her in the OR and clinic again.

Week 6: Allison

I spent the first part of this week running flow cytometry on the T cell samples I stained last week and started learning FlowJo to perform the analysis. Eleana and I also worked on an experimental plan for our next set of experiments and discussed and refined it at lab meeting. We also worked on preparing more gels for T cell activation, and earlier today we extracted and seeded T cells from the spleens and lymph nodes of mice into our gels so they activate over the weekend. We figured out how to make our own coculturing inserts for well plates so T cells and cancer cells could be seeded in different chambers and imaged as they migrate toward each other. We were hoping to buy inserts that would suit these needs, but the shipping would take over a month, so we made our own out of PDMS and Legos. I had another day of shadowing in pathology this week, and I'm always surprised how different cases look even for the same types of breast cancer.

Week 6: Adam

 I made some progress on my research progress this week, since I was able to finish performing the immunofluorescence staining on the samples of discarding adipose tissue that I have been working on. This was really useful, as it gives us a sense of what the expected results are when we start the multiplexed immunofluorescence using the CellScape. I was also able to compare how the IF results change between different patients and different areas of the body, which was really interesting. I also started learning more about techniques for analyzing high resolution imaging data for the multiplexed IF, including some new software and new Python libraries. I also spent some time in the clinic; we even performed a few procedures during the outpatient clinic hours since they didn't require anesthesia. In the clinic I saw a patient who had previously had a fibula flap mandible reconstruction similar to the one I saw a few weeks ago. It was really interesting how different the flap looks once it has had more than a year to heal, which provided insight into the healing process of a more invasive reconstructive procedure. One aspect of the procedures that I have seen in the OR which I find fascinating is the surgical planning process, since the surgeons work together with the patient (in cosmetic cases) to place the incisions precisely in order to get the desired results. 

Week 6: Peter

 I finally made it into some surgeries this week with Tuesday being super busy. I got in a little after 7 and watched a simultaneous liver and kidney transplant with Dr. Samstein. It was surprising how mobile and stretchy all the components of the abdomen were. The tissue retractors were also pretty cool. I am curious how the anesthesiologist's dosing changes when they are temporarily missing some of these organs as kidneys and the liver play large roles in drug filtration and metabolism. I dipped out of this surgery so that I could watch some of Dr. Chandwani's case. His case had been bumped to about 5 pm due to some more pressing transplant cases in the OR. He was going to be removing some of the patients duodenum and possibly performing a whipple depending on the size and spread of the tumor. They quickly performed a diagnostic laparoscopy before opening up her abdomen. Due to a prior gallbladder removal, some of the organs were scarred and fused to one another making it much more difficult to access the duodenum. On Wednesday, I joined one of Dr. Chandawani's PAs on a case with Dr. Rocca. They were using the Da Vinci surgical robot to remove a liver cyst. Dr. Rocca was incredibly good at navigating the environment and almost had a proprioceptive understanding of where the arms were. He was using the shaft of tools to hold tissue back as he made cuts with the other tools. I also got to see one of his residents run the machine and see how they differed in techniques. The PA acted almost like a fifth arm to the machine and would provide suction where needed while also changing tools or dropping in new supplies like absorbent 'cigars'. On Friday I got to scrub in at another Dr. Rocca procedure. They were respecting a large portion of the liver due to cancer. They used this cool ultrasonic ablation tool to do most of the cutting and then would come in with the LigaSure to cut and seal the blood vessels that remained. It was a delicate operation working in such close proximity to the hepatic artery, vein, and the vena cava.